Yaosen Min#, Ye Wei#, Peizhuo Wang#, Xiaoting Wang, Han Li, Nian Wu, Stefan Bauer, Shuxin Zheng, Yu Shi, Yingheng Wang, Ji Wu, Dan Zhao*, Jianyang Zeng* From static to dynamic structures: Improving binding affinity prediction with graph-based deep learning,Advanced Science,2024, 11(40):e2405404

Tingzhong Tian#, Shuya Li#, Ziting Zhang, Lin Chen, Ziheng Zou, Dan Zhao*, Jianyang Zeng* Benchmarking compound activity prediction for real-world drug discovery applications,Communications Chemistry,2024, 7(1):127

Peizhuo Wang, Xiao Wen, Han Li, Peng Lang, Shuya Li, Yipin Lei, Hantao Shu, Lin Gao, Dan Zhao*, Jianyang Zeng* Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON,Nature Communications,2023, 14(1):8459

Han Li, Ruotian Zhang, Yaoseng Min, Dacheng Ma, Dan Zhao*, Jianyang Zeng* A knowledge-guided pre-training framework for improving molecular representation learning,Nature Communications,2023, 14(1):7568

Shuya Li, Tingzhong Tian, Ziting Zhang, Ziheng Zou, Dan Zhao*, Jianyang Zeng* PocketAnchor: Learning structure-based pocket representations for protein-ligand interaction prediction,Cell Systems,2023, 14(8):692-705

Han Li, Xinyi Zhao, Shuya Li, Fangping Wan, Dan Zhao*, Jianyang Zeng* Improving molecular property prediction through a task similarity enhanced transfer learning strategy,iScience,2022, 25(10):105231

Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng, Jianzhu Ma Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data,Briefings in Bioinformatics,23(5):bbac389

Yipin Lei, Shuya Li, Ziyi Liu, Fangping Wan, Tingzhong Tian, Shao Li, Dan Zhao*, Jianyang Zeng* A deep-learning framework for multi-level peptide–protein interaction prediction,Nature Communications,2021, 12(1):5465

Hailin Hu#, Xianggen Liu#, An Xiao, YangYang Li, Chengdong Zhang, Tao Jiang, Dan Zhao, Sen Song, Jianyang Zeng Riboexp: an interpretable reinforcement learning framework for ribosome density modeling,Briefings in Bioinformatics,2021, 22(5):bbaa412

Dan Zhao#, Weifan Xu#, Xiaofan Zhang#, Xiaoting Wang, Enming Yuan, Yuanpeng Xiong, Shenyang Wu, Shuya Li, Nian Wu, Tingzhong Tian, Xiaolong Feng, Hantao Shu, Peng Lang, Xiaokun Shen, Haitao Li, Pilong Li, Jianyang Zeng Understanding the phase separation characteristics of nucleocapsid protein provides a new therapeutic opportunity against SARS-CoV-2,Protein & Cell,2021, 12(9):734–740

Yuanpeng Xiong#, Xuan He#, Dan Zhao, Tingzhong Tian, Lixiang Hong, Tao Jiang, Jianyang Zeng Modelling Multi-species RNA Modification through Multi-task Curriculum Learning,Nucleic Acids Research,49(7):3719–3734

Tingzhong Tian, Shuya Li, Peng Lang, Dan Zhao*, Jianyang Zeng* Full-length ribosome density prediction by a multi-input and multi-output model,PLoS Computational Biology,2021, 17(3):e1008842

Peiyuan Feng#, An Xiao#, Meng Fang, Fangping Wan, Shuya Li, Peng Lang, Dan Zhao*, Jianyang Zeng* A novel machine learning based framework for modeling transcription elongation,Proc Natl Acad Sci USA,2021, 118(6):e2007450118